Contacts of the helix formed by residues 825 - 836 (chain M) in PDB entry 6G0L
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 825 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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626M TYR* 5.4 6.3 - - + +
655M LEU 5.5 0.2 - - - -
656M LYS* 3.8 40.2 - - + +
659M SER* 4.0 10.1 - - - +
793M TRP* 6.0 0.4 - - + -
824M THR* 1.3 82.7 - - - +
826M GLU* 1.3 79.4 + - + +
828M GLU* 3.2 23.8 + - + +
829M VAL* 3.6 18.3 + - + +
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Residues in contact with GLU 826 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656M LYS* 2.9 27.4 - - - +
659M SER* 3.4 13.8 - - - -
660M ASN* 4.9 5.1 + - - -
790M ASP* 4.4 26.0 - - + +
791M SER* 5.5 9.6 - - - +
820M VAL* 6.0 1.1 - - + -
821M SER* 3.7 20.4 - - - +
824M THR* 2.9 24.1 + - - +
825M VAL* 1.3 87.6 + - + +
827M GLU* 1.3 60.6 + - - +
829M VAL* 3.3 10.2 + - + +
830M LEU* 2.9 27.4 + - - +
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Residues in contact with GLU 827 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615M ARG* 5.3 7.9 - - - +
820M VAL* 4.9 11.6 - - + +
821M SER 3.0 12.3 + - - +
822M LYS* 5.9 1.3 - - + +
823M ASP* 3.6 9.8 - - - +
824M THR* 2.8 54.9 + - - +
826M GLU* 1.3 73.8 - - - +
828M GLU* 1.3 78.7 + - - +
830M LEU* 3.3 10.8 + - + +
831M GLU* 2.9 35.8 + - + +
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Residues in contact with GLU 828 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824M THR 4.1 4.6 - - - +
825M VAL* 3.2 27.2 - - + +
826M GLU 3.3 0.2 - - - -
827M GLU* 1.3 101.6 - - - +
829M VAL* 1.3 62.3 + - + +
831M GLU* 3.3 8.1 + - - +
832M ARG* 2.9 36.9 + - + +
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Residues in contact with VAL 829 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791M SER* 5.4 6.5 - - - +
793M TRP* 3.5 81.7 - - + +
825M VAL* 3.6 17.7 - - + +
826M GLU* 3.3 10.9 + - - +
828M GLU* 1.3 77.9 - - + +
830M LEU* 1.3 57.9 + - - +
832M ARG* 3.4 10.9 + - + +
833M ALA* 2.9 27.8 + - + +
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Residues in contact with LEU 830 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613M ILE* 6.1 1.1 - - + -
791M SER* 3.4 26.6 - - - +
798M ASP* 5.5 1.3 - - - +
818M ARG* 4.5 12.6 - - - +
820M VAL* 4.4 30.1 - - + -
826M GLU 2.9 17.8 + - - +
827M GLU* 3.5 9.0 - - + +
828M GLU 3.2 0.2 - - - -
829M VAL* 1.3 77.7 - - - +
831M GLU* 1.3 60.9 + - - +
833M ALA* 3.2 11.7 + - + +
834M ARG* 2.9 59.6 + - + +
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Residues in contact with GLU 831 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615M ARG* 5.8 1.9 + - - -
827M GLU* 2.9 24.6 + - + +
828M GLU* 3.7 6.7 - - - +
830M LEU* 1.3 80.8 - - - +
832M ARG* 1.3 57.7 + - + +
834M ARG* 3.0 15.9 + - - +
835M LYS* 2.9 43.1 + - - +
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Residues in contact with ARG 832 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J T 5.4 8.9 + - - -
793M TRP* 5.6 8.1 - - - +
828M GLU* 2.9 27.6 + - + +
829M VAL* 3.7 13.0 - - + +
831M GLU* 1.3 76.8 - - + +
833M ALA* 1.3 60.0 + - - +
835M LYS* 3.5 18.1 + - + +
836M LYS* 3.4 34.0 + - - +
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Residues in contact with ALA 833 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791M SER* 6.0 3.1 - - - -
794M ASN 4.8 6.1 - - - +
795M PRO* 3.8 30.4 - - + +
829M VAL* 2.9 15.2 + - + +
830M LEU* 3.2 18.1 + - + +
832M ARG* 1.3 77.5 - - - +
834M ARG* 1.3 62.9 + - - +
836M LYS* 3.5 11.5 + - - +
837M MET* 3.4 20.6 + - - +
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Residues in contact with ARG 834 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818M ARG* 3.9 32.7 - - - +
830M LEU* 2.9 39.9 + - + +
831M GLU* 3.0 18.8 + - - +
833M ALA* 1.3 76.5 - - - +
835M LYS* 1.3 64.5 + - + +
837M MET* 3.2 29.1 + - - +
838M ILE* 3.4 20.9 + - + +
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Residues in contact with LYS 835 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831M GLU* 2.9 30.1 + - - +
832M ARG* 3.7 20.0 - - + +
833M ALA 3.3 0.2 - - - -
834M ARG* 1.3 78.5 - - + +
836M LYS* 1.3 59.3 + - + +
837M MET 3.2 0.4 - - - -
838M ILE* 3.4 28.5 - - + +
839M LEU* 4.9 1.7 + - - +
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Residues in contact with LYS 836 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J C 5.6 4.9 + - - -
544M PRO* 5.7 3.8 - - - +
546M GLN* 4.9 9.5 - - - +
547M ASN* 3.7 41.3 + - + +
793M TRP* 5.5 4.8 + - - -
794M ASN* 5.3 1.0 - - - +
795M PRO* 3.5 39.2 - - + +
796M GLN* 5.5 2.3 + - - -
832M ARG* 3.4 23.4 + - - +
833M ALA* 3.5 8.7 + - - +
834M ARG 3.3 0.6 - - - -
835M LYS* 1.3 77.0 - - + +
837M MET* 1.3 58.4 + - - +
839M LEU* 4.6 10.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il